347 research outputs found
Critical Networks Exhibit Maximal Information Diversity in Structure-Dynamics Relationships
Network structure strongly constrains the range of dynamic behaviors
available to a complex system. These system dynamics can be classified based on
their response to perturbations over time into two distinct regimes, ordered or
chaotic, separated by a critical phase transition. Numerous studies have shown
that the most complex dynamics arise near the critical regime. Here we use an
information theoretic approach to study structure-dynamics relationships within
a unified framework and how that these relationships are most diverse in the
critical regime
Explaining the rise of 'human rights' in analyses of Sino-African relations
Popular perceptions of China and its global role are often shaped by two words: 'made in'. Yet this vision of China that focuses primarily on Beijing as a coming economic superpower is relatively new, and it is not that long ago that two other words tended to dominate debates on and discourses of China: 'human rights'. To be sure, real interest in human rights in China was never the only issue in other states' relations with China, nor consistently pursued throughout the years (Nathan, 1994). Nor did human rights totally subsequently disappear from the political agenda.1 Nevertheless, the rhetorical importance of human rights - perhaps best epitomised by the narrow defeat of resolutions condemning Chinese policy in 1995 at the Human Rights Council in Geneva - stands in stark contrast to the relative silence thereafter as the bottom line of most states' relations with Beijing took on ever greater economic dimensions
Characterization of growth and metabolism of the haloalkaliphile Natronomonas pharaonis
Natronomonas pharaonis is an archaeon adapted to two extreme conditions: high salt concentration and alkaline pH. It has become one of the model organisms for the study of extremophilic life. Here, we present a genome-scale, manually curated metabolic reconstruction for the microorganism. The reconstruction itself represents a knowledge base of the haloalkaliphile's metabolism and, as such, would greatly assist further investigations on archaeal pathways. In addition, we experimentally determined several parameters relevant to growth, including a characterization of the biomass composition and a quantification of carbon and oxygen consumption. Using the metabolic reconstruction and the experimental data, we formulated a constraints-based model which we used to analyze the behavior of the archaeon when grown on a single carbon source. Results of the analysis include the finding that Natronomonas pharaonis, when grown aerobically on acetate, uses a carbon to oxygen consumption ratio that is theoretically near-optimal with respect to growth and energy production. This supports the hypothesis that, under simple conditions, the microorganism optimizes its metabolism with respect to the two objectives. We also found that the archaeon has a very low carbon efficiency of only about 35%. This inefficiency is probably due to a very low P/O ratio as well as to the other difficulties posed by its extreme environment
Melt analysis of mismatch amplification mutation assays (melt-MAMA): a functional study of a cost-effective SNP genotyping assay in bacterial models.
Single nucleotide polymorphisms (SNPs) are abundant in genomes of all species and biologically informative markers extensively used across broad scientific disciplines. Newly identified SNP markers are publicly available at an ever-increasing rate due to advancements in sequencing technologies. Efficient, cost-effective SNP genotyping methods to screen sample populations are in great demand in well-equipped laboratories, but also in developing world situations. Dual Probe TaqMan assays are robust but can be cost-prohibitive and require specialized equipment. The Mismatch Amplification Mutation Assay, coupled with melt analysis (Melt-MAMA), is flexible, efficient and cost-effective. However, Melt-MAMA traditionally suffers from high rates of assay design failures and knowledge gaps on assay robustness and sensitivity. In this study, we identified strategies that improved the success of Melt-MAMA. We examined the performance of 185 Melt-MAMAs across eight different pathogens using various optimization parameters. We evaluated the effects of genome size and %GC content on assay development. When used collectively, specific strategies markedly improved the rate of successful assays at the first design attempt from ~50% to ~80%. We observed that Melt-MAMA accurately genotypes across a broad DNA range (~100 ng to ~0.1 pg). Genomic size and %GC content influence the rate of successful assay design in an independent manner. Finally, we demonstrated the versatility of these assays by the creation of a duplex Melt-MAMA real-time PCR (two SNPs) and conversion to a size-based genotyping system, which uses agarose gel electrophoresis. Melt-MAMA is comparable to Dual Probe TaqMan assays in terms of design success rate and accuracy. Although sensitivity is less robust than Dual Probe TaqMan assays, Melt-MAMA is superior in terms of cost-effectiveness, speed of development and versatility. We detail the parameters most important for the successful application of Melt-MAMA, which should prove useful to the wider scientific community
Identifying topological edge states in 2D optical lattices using light scattering
We recently proposed in a Letter [Physical Review Letters 108 255303] a novel
scheme to detect topological edge states in an optical lattice, based on a
generalization of Bragg spectroscopy. The scope of the present article is to
provide a more detailed and pedagogical description of the system - the
Hofstadter optical lattice - and probing method. We first show the existence of
topological edge states, in an ultra-cold gas trapped in a 2D optical lattice
and subjected to a synthetic magnetic field. The remarkable robustness of the
edge states is verified for a variety of external confining potentials. Then,
we describe a specific laser probe, made from two lasers in Laguerre-Gaussian
modes, which captures unambiguous signatures of these edge states. In
particular, the resulting Bragg spectra provide the dispersion relation of the
edge states, establishing their chiral nature. In order to make the Bragg
signal experimentally detectable, we introduce a "shelving method", which
simultaneously transfers angular momentum and changes the internal atomic
state. This scheme allows to directly visualize the selected edge states on a
dark background, offering an instructive view on topological insulating phases,
not accessible in solid-state experiments.Comment: 17 pages, 10 figures. Revised and extended version, to appear in EJP
Special Topic for the special issue on "Novel Quantum Phases and Mesoscopic
Physics in Quantum Gases". Extended version of arXiv:1203.124
Bistability in Apoptosis by Receptor Clustering
Apoptosis is a highly regulated cell death mechanism involved in many
physiological processes. A key component of extrinsically activated apoptosis
is the death receptor Fas, which, on binding to its cognate ligand FasL,
oligomerize to form the death-inducing signaling complex. Motivated by recent
experimental data, we propose a mathematical model of death ligand-receptor
dynamics where FasL acts as a clustering agent for Fas, which form locally
stable signaling platforms through proximity-induced receptor interactions.
Significantly, the model exhibits hysteresis, providing an upstream mechanism
for bistability and robustness. At low receptor concentrations, the bistability
is contingent on the trimerism of FasL. Moreover, irreversible bistability,
representing a committed cell death decision, emerges at high concentrations,
which may be achieved through receptor pre-association or localization onto
membrane lipid rafts. Thus, our model provides a novel theory for these
observed biological phenomena within the unified context of bistability.
Importantly, as Fas interactions initiate the extrinsic apoptotic pathway, our
model also suggests a mechanism by which cells may function as bistable
life/death switches independently of any such dynamics in their downstream
components. Our results highlight the role of death receptors in deciding cell
fate and add to the signal processing capabilities attributed to receptor
clustering.Comment: Accepted by PLoS Comput Bio
A Study of the Quasi-elastic (e,e'p) Reaction on C, Fe and Au
We report the results from a systematic study of the quasi-elastic (e,e'p)
reaction on C, Fe and Au performed at Jefferson Lab. We
have measured nuclear transparency and extracted spectral functions (corrected
for radiation) over a Q range of 0.64 - 3.25 (GeV/c) for all three
nuclei. In addition we have extracted separated longitudinal and transverse
spectral functions at Q of 0.64 and 1.8 (GeV/c) for these three nuclei
(except for Au at the higher Q). The spectral functions are
compared to a number of theoretical calculations. The measured spectral
functions differ in detail but not in overall shape from most of the
theoretical models. In all three targets the measured spectral functions show
considerable excess transverse strength at Q = 0.64 (GeV/c), which is
much reduced at 1.8 (GeV/c).Comment: For JLab E91013 Collaboration, 19 pages, 20 figures, 3 table
Measurements of Deuteron Photodisintegration up to 4.0 GeV
The first measurements of the differential cross section for the d(gamma,p)n
reaction up to 4.0 GeV were performed at Continuous Electron Beam Accelerator
Facility (CEBAF) at Jefferson Lab. We report the cross sections at the proton
center-of-mass angles of 36, 52, 69 and 89 degrees. These results are in
reasonable agreement with previous measurements at lower energy. The 89 and 69
degree data show constituent-counting-rule behavior up to 4.0 GeV photon
energy. The 36 and 52 degree data disagree with the counting rule behavior. The
quantum chromodynamics (QCD) model of nuclear reactions involving reduced
amplitudes disagrees with the present data.Comment: 5 pages (REVTeX), 1 figure (postscript
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